Yaff Documentation

Yaff stands for “Yet another force field”. It is a pythonic force-field (FF) code used at the Center for Molecular Modeling (CMM) to test-drive new FF models. The original motivation to develop Yaff was to provide a good reference implementation of the force fields developed at the CMM. In its current version, Yaff is general and flexible enough to handle a large variety of force field models.

User Guide

This guide is a gentle introduction to Yaff with many examples.

• 1. Features and release notes
  • 1.1. Features
  • 1.2. Release notes
• 2. Installation
  • 2.1. Disclaimer
  • 2.2. External dependencies
  • 2.3. Installation
  • 2.4. Test your installation
• 3. If you encounter a problem
• 4. How to cite Yaff
• 5. Overview of Yaff
• 6. Representation of a molecular system
  • 6.1. Introduction
  • 6.2. Working with the System class
• 7. The ATSELECT language
• 8. Force-field models
  • 8.1. Introduction
  • 8.2. Force field parameter file format
  • 8.3. Example force field file
  • 8.4. Beyond force field parameter files
• 9. Exploring the phase space
  • 9.1. Introduction
  • 9.2. Molecular Dynacmis
  • 9.3. Geometry optimization
  • 9.4. Harmonic approximations
• 10. Trajectory Analysis
  • 10.1. Slicing the data
  • 10.2. Basic analysis
  • 10.3. Advanced analysis
  • 10.4. Post-processing external trajectory data
• 11. Tuning force field parameters

Tutorials

• 1. Yaff experiments on alpha quartz with the BKS potential
  • 1.1. Introduction
  • 1.2. Preparation
  • 1.3. Bulk modulus
  • 1.4. Thermal expansion
  • 1.5. References

Reference Guide

This guide is mostly generated automatically based on the doc strings in the source code.

• 1. yaff – YAFF - Yet another force field
  • 1.1. yaff.atselect – The ATSELECT language
  • 1.2. yaff.log – Screen logger
  • 1.3. yaff.system – Representation of a molecular systems
  • 1.4. yaff.version – Do not edit this file, versioning is governed by git describe --tags and setup.py.
• 2. yaff.pes – Force-field potential energy surfaces (PESs)
  • 2.1. yaff.pes.dlist – Short-range neighbor lists for covalent energy terms
  • 2.2. yaff.pes.ff – Force field models
  • 2.3. yaff.pes.generator – Automatically generate force field models
  • 2.4. yaff.pes.iclist – Internal-coordinate lists for covalent energy terms
  • 2.5. yaff.pes.nlist – Neighbor lists for pairwise (non-bonding) interactions
  • 2.6. yaff.pes.parameters – Object-oriented representation of parameter files
  • 2.7. yaff.pes.scaling – Short-range scaling of pairwise interactions
  • 2.8. yaff.pes.vlist – Module for the complete list of covalent energy terms.
• 3. yaff.sampling – Phase-space sampling
  • 3.1. yaff.sampling.dof – Abstraction layer for degrees of freedom
  • 3.2. yaff.sampling.harmonic – Harmonic models
  • 3.3. yaff.sampling.io – Trajectory writers
  • 3.4. yaff.sampling.iterative – Base class for iterative algorithms
  • 3.5. yaff.sampling.npt – Barostats
  • 3.6. yaff.sampling.nvt – Thermostats
  • 3.7. yaff.sampling.opt – Geometry/Cell optimization
  • 3.8. yaff.sampling.trajectory – Computations on a reference trajectory
  • 3.9. yaff.sampling.utils – Auxiliary routines for initial velocities
  • 3.10. yaff.sampling.verlet – Generic Verlet integrator
• 4. yaff.analysis – Trajectory analysis
  • 4.1. yaff.analysis.basic – Basic trajectory analysis routines
  • 4.2. yaff.analysis.blav – The block-average method
  • 4.3. yaff.analysis.diffusion – Diffusion constants
  • 4.4. yaff.analysis.hook – Abstract hook implementation for trajectory analysis
  • 4.5. yaff.analysis.pca – Toolkit for Principal Component Analysis (PCA)
  • 4.6. yaff.analysis.rdf – Radial distribution functions
  • 4.7. yaff.analysis.spectrum – Spectral analysis and autocorrelation functions
  • 4.8. yaff.analysis.utils – Auxiliary analysis routines
• 5. yaff.conversion – Conversion of external trajectory data
  • 5.1. yaff.conversion.common – Tools for writing trajectory data
  • 5.2. yaff.conversion.cp2k – CP2K Files
  • 5.3. yaff.conversion.dlpoly – DLPOLY Files
  • 5.4. yaff.conversion.gaussian – Gaussian09 BOMD log Files
  • 5.5. yaff.conversion.xyz – XYZ Files
• 6. yaff.tune – Tools to calibrated FF parameters
  • 6.1. yaff.tune.cost – Cost functions for the calibration of FF parameters
  • 6.2. yaff.tune.transform – Specification of variables in a parameters file

Development information

The git repository is hosted at Github.

• 1. Informal TODO list
• 2. The back-propagation algorithm for the computation of energy derivatives

Indices and tables

• Index
• Module Index
• Search Page